The yam (Dioscorea L.) flora of the Comoro Archipelago comprises seven cultivated, introduced or widespread species and a single endemic, D. comorensis R.Knuth, previously known only from the male type specimen but very recently rediscovered with both male and female plants. Specimens from Mayotte are shown to belong to a distinct species, which is described and illustrated. Dioscorea mayottensis Wilkin differs from D. comorensis in its less persistent pubescence, male inflorescence morphology, pedicel length, torus shape and filament morphology. Dioscorea comorensis is described from the type, two newly identified specimens and specimens and photographs from the very recently rediscovered populations. Both species have edible tubers. Preliminary conservation status assessments are given; D. comorensis may face the greater threat. The inflorescence morphology and relationships of both species to those from Madagascar are discussed. A key based on vegetative characters is provided to facilitate the identification of the yams of the Comoro Archipelago.